A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWaveletTransform.h>

Classes
struct	BoxElement
	Internally used data structure. More...
class	TransSpectrum
	Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU and avoids unnecessary memory moves. The class is tailored on the isotope wavelet transform and is in general not applicable on similar - but different - situations. More...
Public Types
typedef std::multimap< UInt, BoxElement >	Box
	Key: RT index, value: BoxElement.
Public Member Functions
	IsotopeWaveletTransform (const DoubleReal min_mz, const DoubleReal max_mz, const UInt max_charge, const Size max_scan_size=0, const bool use_cuda=false, const bool hr_data=false, const String intenstype="ref")
	Constructor.
virtual	~IsotopeWaveletTransform ()
	Destructor.
virtual void	getTransform (MSSpectrum< PeakType > &c_trans, const MSSpectrum< PeakType > &c_ref, const UInt c)
	Computes the isotope wavelet transform of charge state `c`.
virtual void	getTransformHighRes (MSSpectrum< PeakType > &c_trans, const MSSpectrum< PeakType > &c_ref, const UInt c)
	Computes the isotope wavelet transform of charge state `c`.
virtual void	identifyCharge (const MSSpectrum< PeakType > &candidates, const MSSpectrum< PeakType > &ref, const UInt scan_index, const UInt c, const DoubleReal ampl_cutoff, const bool check_PPMs)
	Given an isotope wavelet transformed spectrum `candidates`, this function assigns to every significant pattern its corresponding charge state and a score indicating the reliability of the prediction. The result of this process is stored internally. Important: Before calling this function, apply updateRanges() to the original map.
virtual void	initializeScan (const MSSpectrum< PeakType > &c_ref, const UInt c=0)
void	updateBoxStates (const MSExperiment< PeakType > &map, const Size scan_index, const UInt RT_interleave, const UInt RT_votes_cutoff, const Int front_bound=-1, const Int end_bound=-1)
	A function keeping track of currently open and closed sweep line boxes. This function is used by the isotope wavelet feature finder and must be called for each processed scan.
void	mergeFeatures (IsotopeWaveletTransform< PeakType > *later_iwt, const UInt RT_interleave, const UInt RT_votes_cutoff)
FeatureMap< Feature >	mapSeeds2Features (const MSExperiment< PeakType > &map, const UInt RT_votes_cutoff)
	Filters the candidates further more and maps the internally used data structures to the OpenMS framework.
virtual std::multimap < DoubleReal, Box >	getClosedBoxes ()
	Returns the closed boxes.
DoubleReal	getLinearInterpolation (const typename MSSpectrum< PeakType >::const_iterator &left_iter, const DoubleReal mz_pos, const typename MSSpectrum< PeakType >::const_iterator &right_iter)
	Computes a linear (intensity) interpolation.
DoubleReal	getLinearInterpolation (const DoubleReal mz_a, const DoubleReal intens_a, const DoubleReal mz_pos, const DoubleReal mz_b, const DoubleReal intens_b)
	Computes a linear (intensity) interpolation.
DoubleReal	getSigma () const
void	setSigma (const DoubleReal sigma)
virtual void	computeMinSpacing (const MSSpectrum< PeakType > &c_ref)
DoubleReal	getMinSpacing () const
Size	getMaxScanSize () const
Protected Member Functions
	IsotopeWaveletTransform ()
	Default Constructor.
void	sampleTheCMarrWavelet_ (const MSSpectrum< PeakType > &scan, const Int wavelet_length, const Int mz_index, const UInt charge)
virtual DoubleReal	scoreThis_ (const TransSpectrum &candidate, const UInt peak_cutoff, const DoubleReal seed_mz, const UInt c, const DoubleReal ampl_cutoff)
	Given a candidate for an isotopic pattern, this function computes the corresponding score.
virtual DoubleReal	scoreThis_ (const MSSpectrum< PeakType > &candidate, const UInt peak_cutoff, const DoubleReal seed_mz, const UInt c, const DoubleReal ampl_cutoff)
	Given a candidate for an isotopic pattern, this function computes the corresponding score.
virtual bool	checkPositionForPlausibility_ (const TransSpectrum &candidate, const MSSpectrum< PeakType > &ref, const DoubleReal seed_mz, const UInt c, const UInt scan_index, const bool check_PPMs, const DoubleReal transintens, const DoubleReal prev_score)
	A ugly but necessary function to handle "off-by-1-Dalton predictions" due to idiosyncrasies of the data set (in comparison to the averagine model).
virtual bool	checkPositionForPlausibility_ (const MSSpectrum< PeakType > &candidate, const MSSpectrum< PeakType > &ref, const DoubleReal seed_mz, const UInt c, const UInt scan_index, const bool check_PPMs, const DoubleReal transintens, const DoubleReal prev_score)
	A ugly but necessary function to handle "off-by-1-Dalton predictions" due to idiosyncrasies of the data set (in comparison to the averagine model).
virtual std::pair< DoubleReal, DoubleReal >	checkPPMTheoModel_ (const MSSpectrum< PeakType > &ref, const DoubleReal c_mz, const UInt c)
DoubleReal	getAvIntens_ (const TransSpectrum &scan)
	Computes the average (transformed) intensity (neglecting negative values) of `scan`.
DoubleReal	getAvIntens_ (const MSSpectrum< PeakType > &scan)
	Computes the average intensity (neglecting negative values) of `scan`.
DoubleReal	getSdIntens_ (const TransSpectrum &scan, const DoubleReal mean)
	Computes the standard deviation (neglecting negative values) of the (transformed) intensities of `scan`.
DoubleReal	getSdIntens_ (const MSSpectrum< PeakType > &scan, const DoubleReal mean)
	Computes the standard deviation (neglecting negative values) of the intensities of `scan`.
virtual void	push2Box_ (const DoubleReal mz, const UInt scan, UInt c, const DoubleReal score, const DoubleReal intens, const DoubleReal rt, const UInt MZ_begin, const UInt MZ_end, const DoubleReal ref_intens)
	Inserts a potential isotopic pattern into an open box or - if no such box exists - creates a new one.
virtual void	push2TmpBox_ (const DoubleReal mz, const UInt scan, UInt charge, const DoubleReal score, const DoubleReal intens, const DoubleReal rt, const UInt MZ_begin, const UInt MZ_end)
	Essentially the same function as.
DoubleReal	getAvMZSpacing_ (const MSSpectrum< PeakType > &scan)
	Computes the average MZ spacing of `scan`.
void	clusterSeeds_ (const TransSpectrum &candidates, const MSSpectrum< PeakType > &ref, const UInt scan_index, const UInt c, const bool check_PPMs)
	Clusters the seeds stored by push2TmpBox_.
virtual void	clusterSeeds_ (const MSSpectrum< PeakType > &candidates, const MSSpectrum< PeakType > &ref, const UInt scan_index, const UInt c, const bool check_PPMs)
	Clusters the seeds stored by push2TmpBox_.
void	extendBox_ (const MSExperiment< PeakType > &map, const Box box)
	A currently still necessary function that extends the box `box` in order to capture also signals whose isotopic pattern is nearly diminishing.
DoubleReal	peptideMassRule_ (const DoubleReal c_mass) const
	Returns the monoisotopic mass (with corresponding decimal values) we would expect at `c_mass`.
DoubleReal	getPPMs_ (const DoubleReal mass_a, const DoubleReal mass_b) const
	Returns the parts-per-million deviation of the masses.
Protected Attributes
std::multimap< DoubleReal, Box >	open_boxes_
std::multimap< DoubleReal, Box >	closed_boxes_
std::multimap< DoubleReal, Box >	end_boxes_
std::multimap< DoubleReal, Box >	front_boxes_
std::vector< std::multimap < DoubleReal, Box > > *	tmp_boxes_
DoubleReal	av_MZ_spacing_
DoubleReal	sigma_
std::vector< DoubleReal >	c_mzs_
std::vector< DoubleReal >	c_spacings_
std::vector< DoubleReal >	psi_
std::vector< DoubleReal >	prod_
std::vector< DoubleReal >	xs_
std::vector< DoubleReal >	interpol_xs_
std::vector< DoubleReal >	interpol_ys_
Size	max_scan_size_
UInt	max_num_peaks_per_pattern_
UInt	max_charge_
UInt	data_length_
bool	hr_data_
String	intenstype_
Int	from_max_to_left_
Int	from_max_to_right_
std::vector< int >	indices_
MSSpectrum< PeakType >	c_sorted_candidate_
DoubleReal	min_spacing_
DoubleReal	max_mz_cutoff_
std::vector< float >	scores_
std::vector< float >	zeros_

Detailed Description

template<typename PeakType>
class OpenMS::IsotopeWaveletTransform< PeakType >

A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform.

Member Typedef Documentation

typedef std::multimap<UInt, BoxElement> Box

Key: RT index, value: BoxElement.

Constructor & Destructor Documentation

IsotopeWaveletTransform	(	const DoubleReal	min_mz,
		const DoubleReal	max_mz,
		const UInt	max_charge,
		const Size	max_scan_size = `0`,
		const bool	use_cuda = `false`,
		const bool	hr_data = `false`,
		const String	intenstype = `"ref"`
	)

Constructor.

Parameters:

	min_mz	The smallest m/z value occurring in your map.
	max_mz	The largest m/z value occurring in your map.
	max_charge	The highest charge state you would like to consider.

~IsotopeWaveletTransform ( ) [virtual]

Destructor.

References NULL, and IsotopeWaveletTransform< PeakType >::tmp_boxes_.

IsotopeWaveletTransform ( ) [protected]

Default Constructor.

Note:: Provided just for inheritance reasons. You should always use the other constructor.

References IsotopeWaveletTransform< PeakType >::av_MZ_spacing_, IsotopeWaveletTransform< PeakType >::hr_data_, IsotopeWaveletTransform< PeakType >::intenstype_, IsotopeWaveletTransform< PeakType >::max_mz_cutoff_, IsotopeWaveletTransform< PeakType >::max_num_peaks_per_pattern_, IsotopeWaveletTransform< PeakType >::max_scan_size_, and IsotopeWaveletTransform< PeakType >::tmp_boxes_.

Member Function Documentation

bool checkPositionForPlausibility_	(	const TransSpectrum &	candidate,
		const MSSpectrum< PeakType > &	ref,
		const DoubleReal	seed_mz,
		const UInt	c,
		const UInt	scan_index,
		const bool	check_PPMs,
		const DoubleReal	transintens,
		const DoubleReal	prev_score
	)			`[protected, virtual]`

A ugly but necessary function to handle "off-by-1-Dalton predictions" due to idiosyncrasies of the data set (in comparison to the averagine model).

Parameters:

	candidate	The wavelet transformed spectrum containing the candidate.
	ref	The original spectrum containing the candidate.
	seed_mz	The m/z position of the candidate pattern.
	c	The predicted charge state minus 1 (e.g. c=2 means charge state 3) of the candidate.
	scan_index	The index of the scan under consideration (w.r.t. the original map).

References IsotopeWaveletTransform< PeakType >::TransSpectrum::begin(), IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), IsotopeWaveletTransform< PeakType >::TransSpectrum::end(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), MSSpectrum< PeakT >::getRT(), OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, MSSpectrum< PeakT >::MZBegin(), IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), IsotopeWaveletTransform< PeakType >::push2Box_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

Referenced by IsotopeWaveletTransform< PeakType >::clusterSeeds_().

bool checkPositionForPlausibility_	(	const MSSpectrum< PeakType > &	candidate,
		const MSSpectrum< PeakType > &	ref,
		const DoubleReal	seed_mz,
		const UInt	c,
		const UInt	scan_index,
		const bool	check_PPMs,
		const DoubleReal	transintens,
		const DoubleReal	prev_score
	)			`[protected, virtual]`

A ugly but necessary function to handle "off-by-1-Dalton predictions" due to idiosyncrasies of the data set (in comparison to the averagine model).

Parameters:

	candidate	The wavelet transformed spectrum containing the candidate.
	ref	The original spectrum containing the candidate.
	seed_mz	The m/z position of the candidate pattern.
	c	The predicted charge state minus 1 (e.g. c=2 means charge state 3) of the candidate.
	scan_index	The index of the scan under consideration (w.r.t. the original map).

References IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), MSSpectrum< PeakT >::getRT(), OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, MSSpectrum< PeakT >::MZBegin(), IsotopeWaveletTransform< PeakType >::push2Box_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

std::pair< DoubleReal, DoubleReal > checkPPMTheoModel_	(	const MSSpectrum< PeakType > &	ref,
		const DoubleReal	c_mz,
		const UInt	c
	)			`[protected, virtual]`

References IsotopeWaveletTransform< PeakType >::getPPMs_(), OpenMS::Constants::IW_PROTON_MASS, MSSpectrum< PeakT >::MZBegin(), OpenMS::Constants::PEPTIDE_MASS_RULE_THEO_PPM_BOUND, and IsotopeWaveletTransform< PeakType >::peptideMassRule_().

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_().

void clusterSeeds_	(	const TransSpectrum &	candidates,
		const MSSpectrum< PeakType > &	ref,
		const UInt	scan_index,
		const UInt	c,
		const bool	check_PPMs
	)			`[protected]`

Clusters the seeds stored by push2TmpBox_.

Parameters:

	candidates	A isotope wavelet transformed spectrum.
	ref	The corresponding original spectrum (w.r.t. `candidates`).
	scan_index	The index of the scan under consideration (w.r.t. the original map).

References IsotopeWaveletTransform< PeakType >::BoxElement::c, IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::BoxElement::intens, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::RT, IsotopeWaveletTransform< PeakType >::BoxElement::score, and IsotopeWaveletTransform< PeakType >::tmp_boxes_.

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge().

void clusterSeeds_	(	const MSSpectrum< PeakType > &	candidates,
		const MSSpectrum< PeakType > &	ref,
		const UInt	scan_index,
		const UInt	c,
		const bool	check_PPMs
	)			`[protected, virtual]`

Clusters the seeds stored by push2TmpBox_.

Parameters:

	candidates	A isotope wavelet transformed spectrum.
	ref	The corresponding original spectrum (w.r.t. `candidates`).
	scan_index	The index of the scan under consideration (w.r.t. the original map).

References IsotopeWaveletTransform< PeakType >::BoxElement::c, IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::BoxElement::intens, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::RT, IsotopeWaveletTransform< PeakType >::BoxElement::score, and IsotopeWaveletTransform< PeakType >::tmp_boxes_.

void computeMinSpacing ( const MSSpectrum< PeakType > & c_ref ) [virtual]

References IsotopeWaveletTransform< PeakType >::min_spacing_.

Referenced by IsotopeWaveletTransform< PeakType >::initializeScan().

void extendBox_	(	const MSExperiment< PeakType > &	map,
		const Box	box
	)			`[protected]`

A currently still necessary function that extends the box box in order to capture also signals whose isotopic pattern is nearly diminishing.

Parameters:

	map	The experimental map.
	box	The box to be extended.

References IsotopeWaveletTransform< PeakType >::push2Box_().

DoubleReal getAvIntens_ ( const TransSpectrum & scan ) [inline, protected]

Computes the average (transformed) intensity (neglecting negative values) of scan.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::size().

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge().

DoubleReal getAvIntens_ ( const MSSpectrum< PeakType > & scan ) [inline, protected]

Computes the average intensity (neglecting negative values) of scan.

DoubleReal getAvMZSpacing_ ( const MSSpectrum< PeakType > & scan ) [inline, protected]

Computes the average MZ spacing of scan.

Parameters:

scan

The scan we are interested in.

virtual std::multimap<DoubleReal, Box> getClosedBoxes ( ) [inline, virtual]

Returns the closed boxes.

References IsotopeWaveletTransform< PeakType >::closed_boxes_.

DoubleReal getLinearInterpolation	(	const typename MSSpectrum< PeakType >::const_iterator &	left_iter,
		const DoubleReal	mz_pos,
		const typename MSSpectrum< PeakType >::const_iterator &	right_iter
	)			`[inline]`

Computes a linear (intensity) interpolation.

Parameters:

	left_iter	The point left to the query.
	mz_pos	The query point.
	right_iter	The point right to the query.

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge().

DoubleReal getLinearInterpolation	(	const DoubleReal	mz_a,
		const DoubleReal	intens_a,
		const DoubleReal	mz_pos,
		const DoubleReal	mz_b,
		const DoubleReal	intens_b
	)			`[inline]`

Computes a linear (intensity) interpolation.

Parameters:

	mz_a	The m/z value of the point left to the query.
	mz_a	The intensity value of the point left to the query.
	mz_pos	The query point.
	mz_b	The m/z value of the point right to the query.
	intens_b	The intensity value of the point left to the query.

Size getMaxScanSize ( ) const [inline]

References IsotopeWaveletTransform< PeakType >::max_scan_size_.

DoubleReal getMinSpacing ( ) const [inline]

References IsotopeWaveletTransform< PeakType >::min_spacing_.

DoubleReal getPPMs_	(	const DoubleReal	mass_a,
		const DoubleReal	mass_b
	)			const `[inline, protected]`

Returns the parts-per-million deviation of the masses.

Parameters:

	mass_a	The first mass.
	mass_b	The second mass.

Referenced by IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_().

DoubleReal getSdIntens_	(	const TransSpectrum &	scan,
		const DoubleReal	mean
	)			`[inline, protected]`

Computes the standard deviation (neglecting negative values) of the (transformed) intensities of scan.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::size().

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge().

DoubleReal getSdIntens_	(	const MSSpectrum< PeakType > &	scan,
		const DoubleReal	mean
	)			`[inline, protected]`

Computes the standard deviation (neglecting negative values) of the intensities of scan.

DoubleReal getSigma ( ) const [inline]

References IsotopeWaveletTransform< PeakType >::sigma_.

void getTransform	(	MSSpectrum< PeakType > &	c_trans,
		const MSSpectrum< PeakType > &	c_ref,
		const UInt	c
	)			`[virtual]`

Computes the isotope wavelet transform of charge state c.

Parameters:

	c_trans	The transform.
	c_ref	The reference spectrum.
	c	The charge state minus 1 (e.g. c=2 means charge state 3) at which you want to compute the transform.

References IsotopeWaveletTransform< PeakType >::from_max_to_left_, IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getValueByLambda(), OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, and IsotopeWaveletTransform< PeakType >::min_spacing_.

Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run().

void getTransformHighRes	(	MSSpectrum< PeakType > &	c_trans,
		const MSSpectrum< PeakType > &	c_ref,
		const UInt	c
	)			`[virtual]`

Computes the isotope wavelet transform of charge state c.

Parameters:

	c_trans	The transform.
	c_ref	The reference spectrum.
	c	The charge state minus 1 (e.g. c=2 means charge state 3) at which you want to compute the transform.

References IsotopeWaveletTransform< PeakType >::from_max_to_left_, IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getValueByLambda(), and OpenMS::Constants::IW_QUARTER_NEUTRON_MASS.

Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run().

void identifyCharge	(	const MSSpectrum< PeakType > &	candidates,
		const MSSpectrum< PeakType > &	ref,
		const UInt	scan_index,
		const UInt	c,
		const DoubleReal	ampl_cutoff,
		const bool	check_PPMs
	)			`[virtual]`

Given an isotope wavelet transformed spectrum candidates, this function assigns to every significant pattern its corresponding charge state and a score indicating the reliability of the prediction. The result of this process is stored internally. Important: Before calling this function, apply updateRanges() to the original map.

Parameters:

candidates

A isotope wavelet transformed spectrum. Entry "number i" in this vector must correspond to the charge-"(i-1)"-transform of its mass signal. (This is exactly the output of the function

See also:: getTransforms.)

Parameters:

	ref	The reference scan (the untransformed raw data) corresponding to `candidates`.
	c	The corrsponding charge state minus 1 (e.g. c=2 means charge state 3)
	scan_index	The index of the scan (w.r.t. to some map) currently under consideration.
	ampl_cutoff	The thresholding parameter. This parameter is the only (and hence a really important) parameter of the isotope wavelet transform. On the basis of `ampl_cutoff` the program tries to distinguish between noise and signal. Please note that it is not a "simple" hard thresholding parameter in the sense of drawing a virtual line in the spectrum, which is then used as a guillotine cut. Maybe you should play around a bit with this parameter to get a feeling about its range. For peptide mass fingerprints on small data sets (like single MALDI-scans e.g.), it makes sense to start `ampl_cutoff=0` or even `ampl_cutoff=-1`, indicating no thresholding at all. Note that also ampl_cutoff=0 triggers (a moderate) thresholding based on the average intensity in the wavelet transform.
	check_PPMs	If enabled, the algorithm will check each monoisotopic mass candidate for its plausibility by computing the ppm difference between this mass and the averagine model.

Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run().

void initializeScan	(	const MSSpectrum< PeakType > &	c_ref,
		const UInt	c = `0`
	)			`[virtual]`

Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run().

FeatureMap< Feature > mapSeeds2Features	(	const MSExperiment< PeakType > &	map,
		const UInt	RT_votes_cutoff
	)

Filters the candidates further more and maps the internally used data structures to the OpenMS framework.

Parameters:

	map	The original map containing the data set to be analyzed.
	max_charge	The maximal charge state under consideration.
	RT_votes_cutoff	See the IsotopeWaveletFF class.

References ConvexHull2D::addPoints(), IsotopeWaveletTransform< PeakType >::closed_boxes_, IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWaveletTransform< PeakType >::intenstype_, OpenMS::Constants::IW_NEUTRON_MASS, OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::max_charge_, MSSpectrum< PeakT >::MZBegin(), BaseFeature::setCharge(), Feature::setConvexHulls(), Peak2D::setIntensity(), Peak2D::setMZ(), Feature::setOverallQuality(), and Peak2D::setRT().

Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run().

void mergeFeatures	(	IsotopeWaveletTransform< PeakType > *	later_iwt,
		const UInt	RT_interleave,
		const UInt	RT_votes_cutoff
	)

DoubleReal peptideMassRule_ ( const DoubleReal c_mass ) const [inline, protected]

Returns the monoisotopic mass (with corresponding decimal values) we would expect at c_mass.

Parameters:

c_mass

The mass for which we would like to know the averagine decimal places.

References OpenMS::Constants::PEPTIDE_MASS_RULE_BOUND, and OpenMS::Constants::PEPTIDE_MASS_RULE_FACTOR.

Referenced by IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_().

void push2Box_	(	const DoubleReal	mz,
		const UInt	scan,
		UInt	c,
		const DoubleReal	score,
		const DoubleReal	intens,
		const DoubleReal	rt,
		const UInt	MZ_begin,
		const UInt	MZ_end,
		const DoubleReal	ref_intens
	)			`[protected, virtual]`

Inserts a potential isotopic pattern into an open box or - if no such box exists - creates a new one.

Parameters:

	mz	The position of the pattern.
	scan	The index of the scan, we are currently analyzing (w.r.t. the data map). This information is necessary for the post-processing (sweep lining).
	charge	The estimated charge state minus 1 (e.g. c=2 means charge state 3) of the pattern.
	score	The pattern's score.
	intens	The intensity at the monoisotopic peak.
	rt	The retention time of the scan (similar to `scan`, but here: no index, but the real value).
	MZ_begin	The starting index of the pattern (m/z) w.r.t. the current scan.
	MZ_end	The end index (w.r.t. the monoisotopic position!) of the pattern (m/z) w.r.t. the current scan.

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), and IsotopeWaveletTransform< PeakType >::extendBox_().

void push2TmpBox_	(	const DoubleReal	mz,
		const UInt	scan,
		UInt	charge,
		const DoubleReal	score,
		const DoubleReal	intens,
		const DoubleReal	rt,
		const UInt	MZ_begin,
		const UInt	MZ_end
	)			`[protected, virtual]`

Essentially the same function as.

See also:: push2Box_. In contrast to; push2Box this function stores its candidates only temporarily. In particular, this function is only used within a single scan transform. After the wavelet transform is computed on that scan, all candidates are pushed by this function and finally clustered together by; clusterSeeds_. Afterwards, a final push by; push2Box_ is performed storing the clustered candidates.

Parameters:

	mz	The position of the pattern.
	scan	The index of the scan, we are currently analyzing (w.r.t. the data map). This information is necessary for the post-processing (sweep lining).
	charge	The estimated charge state minus 1 (e.g. c=2 means charge state 3) of the pattern.
	score	The pattern's score.
	intens	The intensity at the monoisotopic peak.
	rt	The retention time of the scan (similar to `scan`, but here: no index, but the real value).
	MZ_begin	The starting index of the pattern (m/z) w.r.t. the current scan.
	MZ_end	The end index (w.r.t. the monoisotopic position!) of the pattern (m/z) w.r.t. the current scan.

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge().

void sampleTheCMarrWavelet_	(	const MSSpectrum< PeakType > &	scan,
		const Int	wavelet_length,
		const Int	mz_index,
		const UInt	charge
	)			`[inline, protected]`

DoubleReal scoreThis_	(	const MSSpectrum< PeakType > &	candidate,
		const UInt	peak_cutoff,
		const DoubleReal	seed_mz,
		const UInt	c,
		const DoubleReal	ampl_cutoff
	)			`[protected, virtual]`

Given a candidate for an isotopic pattern, this function computes the corresponding score.

Parameters:

	candidate	A isotope wavelet transformed spectrum.
	peak_cutoff	The number of peaks we will consider for the isotopic pattern.
	seed_mz	The predicted position of the monoisotopic peak.
	c	The charge state minus 1 (e.g. c=2 means charge state 3) for which the score should be determined.
	ampl_cutoff	The threshold.

References OpenMS::Constants::IW_HALF_NEUTRON_MASS, OpenMS::Constants::IW_NEUTRON_MASS, and MSSpectrum< PeakT >::MZBegin().

DoubleReal scoreThis_	(	const TransSpectrum &	candidate,
		const UInt	peak_cutoff,
		const DoubleReal	seed_mz,
		const UInt	c,
		const DoubleReal	ampl_cutoff
	)			`[protected, virtual]`

Given a candidate for an isotopic pattern, this function computes the corresponding score.

Parameters:

	candidate	A isotope wavelet transformed spectrum.
	peak_cutoff	The number of peaks we will consider for the isotopic pattern.
	seed_mz	The predicted position of the monoisotopic peak.
	c	The charge state minus 1 (e.g. c=2 means charge state 3) for which the score should be determined.
	ampl_cutoff	The threshold.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::begin(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getMZ(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), OpenMS::Constants::IW_HALF_NEUTRON_MASS, OpenMS::Constants::IW_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::size().

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), and IsotopeWaveletTransform< PeakType >::identifyCharge().

void setSigma ( const DoubleReal sigma ) [inline]

References IsotopeWaveletTransform< PeakType >::sigma_.

void updateBoxStates	(	const MSExperiment< PeakType > &	map,
		const Size	scan_index,
		const UInt	RT_interleave,
		const UInt	RT_votes_cutoff,
		const Int	front_bound = `-1`,
		const Int	end_bound = `-1`
	)

A function keeping track of currently open and closed sweep line boxes. This function is used by the isotope wavelet feature finder and must be called for each processed scan.

Parameters:

	map	The original map containing the data set to be analyzed.
	scan_index	The index of the scan currently under consideration w.r.t. its MS map. This information is necessary to sweep across the map after each scan has been evaluated.
	RT_votes_cutoff	See the IsotopeWaveletFF class.

References IsotopeWaveletTransform< PeakType >::closed_boxes_, IsotopeWaveletTransform< PeakType >::end_boxes_, IsotopeWaveletTransform< PeakType >::front_boxes_, and IsotopeWaveletTransform< PeakType >::open_boxes_.

Referenced by IsotopeWaveletParallelFor< PeakType, FeatureType >::operator()(), and FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run().